Commercial and scientific applications of high-temperature superconducting (HTS) materials are rapidly growing as fabrication and production technologies advance in precision and scale. For example, a Josephson junction (JJ), a weak link between two superconductors, is an active element that serves as the building block of a wide segment of superconducting electronic circuits and devices. Ion milling is one method by which JJs are produced. However, existing processes can potentially damage the superconducting film during JJ formation. A need exists for an efficient method to fabricate large numbers of uniform JJs, or other types of structures, in HTS films without causing damage to the superconducting film.